Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Blood
Cell type
B3
NA
NA

Attributes by original data submitter

Sample

source_name
pre-B cell line B3
cell line
B3
chip antibody
Input DNA
agent
4-OHT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For RNAP2 ChIP, chromatin isolated from fixed nuclei was sonicated and incubated at 4ºC overnight with either Protein A Dynabeads (Invitrogen) coated with rabbit anti-RNAP2 antibody. Single-end high throughput sequencing libraries were prepared from 10ng of ChIP DNA using NEB Ultra DNA Library Prep kit for Illumina, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500. For MNase-seq, chromatin from fixed nuclei was digested with MNase and DNA was purified after digestion. Paired-end high throughput sequencing libraries were prepared from 50ng of digested DNA using NEB Ultra DNA Library Prep kit for Illumina, without size selection steps, and sequenced according to the manufacturer's protocols using Illumina Hi-seq2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
50995545
Reads aligned (%)
98.2
Duplicates removed (%)
12.0
Number of peaks
501 (qval < 1E-05)

mm9

Number of total reads
50995545
Reads aligned (%)
97.9
Duplicates removed (%)
12.0
Number of peaks
574 (qval < 1E-05)

Base call quality data from DBCLS SRA